[gmx-users] Interaction energies between atoms

Hello GMX users, I'm simulation a mixture of polymers, water, and hydrocarbons. I want to calculate the interaction energies of an atom in one of the polymers with another atom in the system. Is there any way to do it in gromacs? Thank you Sam -- Gromacs Users mailing list * Please search the

[gmx-users] Unability to generate toplogy files for T3 & T4 residues from 4lnx.pdb

The universal force field is also not working. how can I generate parameters for such hetero-clusters via gromacs? *Denish PoudyalCDPTU, Nepal* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Automatic calculation of several RDFs

Yes it is, write the script in what ever programming language you use. I have one in python that takes a list of residues and atom names, then generates all the RDFs between those. You can invoke gmx rdf in series, or in parallel (which I was able to do using python). Since your interested in

Re: [gmx-users] AWH with two bias potentials

The cut-off should be a few kT higher than the highest barrier you want to cross. If you have no clue at all 10 kT is often a good initial guess. Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cédric Leyrat Sent: Thursday, February

Re: [gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi Mark, To my knowledge, she's not using CHARMM-related FF's at all -- I think she is using Amber03 (Alyssa, correct me if I'm wrong). Visually and RSMD-wise the trajectory looks totally normal, but is there something specific I should be looking for in the trajectory, either visually or

Re: [gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi, What does the trajectory look like before it crashes? We did recently fix a bug relevant to simulations using CHARMM switching functions on GPUs, if that could be an explanation. We will probably put out a new 2018 version with that fix next week (or so). Mark On Thu., 14 Feb. 2019, 20:26

Re: [gmx-users] AWH with two bias potentials

Thanks Berk, What you're saying makes perfect sense. I should be using one 2D bias instead of two 1D biases. And I should use a cutoff on the free energy. This way gmx awh should generate a 2D PMF. So far I've only modified my .mdp file like this to have one 2D bias, but haven't put the free

[gmx-users] domain decomposition error >60 ns into simulation on a specific machine

Hi all, My student is trying to do a fairly straightforward MD simulation -- a protein complex in water with ions with *no* pull coordinate. It's on an NVidia GPU-based machine and we're running gromacs 2018.3. About 65 ns into the simulation, it dies with: "an atom moved too far between two

Re: [gmx-users] AWH with two bias potentials

Note though, as also noted in the manual, you need to be careful what you wish for. 2D biasing leads to uniform sampling of the requested rectangular area. Often you want to suppress sampling of high free-energy (unphysical or uninteresting) regions in this rectangle by using a cutoff on the

Re: [gmx-users] Make check not passing tests on 2018.5

I can't reproduce this. For me the regressiontests pass with gcc 7.3, AVX_512, double. Roland > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > David Lister > Sent: Tuesday, February

Re: [gmx-users] AWH with two bias potentials

I see now that you used awh-nbias=2 with awh-ndim=1. Thus you asked for 2 independent 1D AWH biases and PMFs. You might be able to get a 2D PMF from that, but that is complicated. I think that what you want is one 2D bias: awh-nbias=1 with awh-ndim=2. Berk

Re: [gmx-users] AWH with two bias potentials

Dear Berk, I do get a set of PMF files at different times for each reaction coordinate from gmx awh. Each file has two columns (x=coordinate 1, y=PMF or x=coordinate 2, y=PMF). My coding and maths skills are quite limited so if you have a script that can convert these data to a 2D format, I

Re: [gmx-users] AWH with two bias potentials

gmx awh writes out the 2D (or any-D) PMF to xvg files for different times. The 1D nature of xvg files is not convenient for visualization though, so you need to write a script to convert it to you favorite 2D data format. I probably have a script somewhere for some 2D format (python?) if you

[gmx-users] AWH with two bias potentials

Dear Gromacs users, I'm simulating a system composed of a transmembrane receptor interacting with a 30 kDa soluble protein that sits on top of it. The receptor has a ~ 20 residue tail that is supposed to interact with the soluble protein. I'm trying to predict the most stable conformation of